The movement order issue shouldn't be a big deal to anybody. The fact is, regardless of how you slice and dice it, the sixth is still a very finale driven symphony. That's why I like playing around with them. Truthfully, some recorded performances work better played back S/A, while others work better played back A/S. It's primarily an issue of tempi and tempo relationships.
Ideally - to my tastes - the first movement and scherzo should work together as a unified Part 1. I'd like to see somebody link the two movements by making the last note of the first movement, also be the first note of the scherzo. You'd have to reduce that last note to just a forte timpani whack. My problem with putting the scherzo just before the finale, is that the last several minutes of the scherzo behave exactly the same as the last six or seven minutes of the finale do - and in the same key, more or less (predominately A-minor). Also, the start of the finale is a bit more shocking when coming off of the Eb Major resolution of the slow movement.